The Catholic Church has withdrawn from plans to create seven shared campuses for Catholic and non-denominational primary schools.
Discussions with North Lanarkshire Council have been ongoing for the last 18 months.
But the Right Rev Joseph Devine, Bishop of Motherwell, said the church could not go ahead because of concerns the schools would lose their identity.
The Scottish Executive had backed moves towards integrated campuses.
Bishop Devine said he had concluded that the council was not prepared to meet the needs of the Catholic community and guarantee the satisfactory provision of Catholic education.
The church has expressed strong opposition to having too many shared facilities and common entrances.
The bishop said: "From the outset of discussions, I expressed my deepest reservations about the council's intention to replace St Aloysius, a school of over 300 pupils, with a new building in which significant facilities would be shared with the non-denominational school."
He added: "It has now become clear that North Lanarkshire Council is not prepared to make the design changes which the diocese has sought.
"Accordingly, I have informed the council that it is pursuing a flawed policy in its determination to promote shared campus provision on this basis in these communities."
Michael McGrath, director of the Scottish Catholic Education Service, said: "When the council eventually provided the building plans, it was clear that the council was determined to maximise the provision of shared facilities."
In February, Scotland's first shared campus between a Roman Catholic and non-denominational secondary school was officially opened.
The shared campus incorporated St David's Roman Catholic High School and Dalkeith High in Midlothian.
A number of primary schools operate shared campuses but the Dalkeith secondary schools were the first in Scotland to do so.
About 1,700 pupils study on the campus, which also includes Saltersgate special school.
As well as their buildings the schools share a number of resources including office accommodation, a library, dining facilities and sports facilities.
Jack McConnell was joined by Cardinal Keith O'Brien and the Very Reverend Dr John Cairns, former moderator of the Church of Scotland for the official opening ceremony.